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In silico prediction of 3D structure of Mn superoxide dismutase of Scylla serrata and its binding properties with inhibitors

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Abstract

In the present study, we used computational methods to model crab and rat MnSOD using the crystal structure of MnSOD from Homo sapiens (PDB code: 1MSD) as template by comparative modeling approach. We performed molecular dynamics simulations to study dynamic behavior of the crab MnSOD. The modeled proteins were validated and subjected to molecular docking analyses. Molecular docking tool was used to elucidate a comparative binding mode of the crab and rat SOD with potent inhibitors of SOD such as hydrogen peroxide (H2O2), potassium cyanide (KCN) and sodium dodecyl sulphate (SDS). The predicted valid structure of crab MnSOD did not show any interaction with KCN but close interaction with H2O2 and SDS. A possible inhibitory mechanism of SDS and H2O2 due to their interaction with the amino acids present in the active site of the MnSOD of the above two animals are elucidated. This allowed us to predict the binding modes of the proteins to elucidate probable mode of action and sites of interference.

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Author notes

  1. Biswaranjan Paital

    Present address: Biochemical Adaptation Lab., Department of Zoology, Banaras Hindu University, Varanasi, 221005, UP, India

  2. Gagan Bihari Nityananda Chainy

    Present address: Imgenex India Pvt. Ltd., E-5, Infocity, Bhubaneswar, 751024, India

Authors and Affiliations

  1. Department of Zoology, Utkal University, Bhubaneswar, 751004, India

    Biswaranjan Paital & Gagan Bihari Nityananda Chainy

  2. Bioinformatics Centre, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India

    Sunil Kumar

  3. Jacob School of Biotechnology and Bioengineering, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad, 211007, India

    Rohit Farmer

  4. Department of Biotechnology, Utkal University, Bhubaneswar, 751004, India

    Gagan Bihari Nityananda Chainy

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  1. Biswaranjan Paital
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  2. Sunil Kumar
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  4. Gagan Bihari Nityananda Chainy
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Correspondence to Sunil Kumar.

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Paital, B., Kumar, S., Farmer, R. et al. In silico prediction of 3D structure of Mn superoxide dismutase of Scylla serrata and its binding properties with inhibitors. Interdiscip Sci Comput Life Sci 5, 69–76 (2013). https://doi.org/10.1007/s12539-013-0150-4

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  • DOI: https://doi.org/10.1007/s12539-013-0150-4

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